Exam 1 Flashcards
What is a virus structurally?
a genome designed for self-replication, surrounded by a protective protein shell called a capsid
What are its (the virus) central purposes?
to safely move its genome around and make more of itself
What is meant by it being an obligate intracellular parasite?
Viruses cannot metabolize on their own, and therefore need to use resources from a living cell. More specifically, a virus needs to be inside of a cell to make more of itself
Know the basic sizes of viruses when compared to host cells
extremely small; 10-1000x smaller than its host cell
Why are they not alive?
Viruses have some living characteristics, but ultimately they cannot perform independent metabolism and therefore are not considered alive
What is meant by the statement that they are ubiquitous?
Essentially everything around us is affected by viruses. They’re found in high concentrations in soil, water, and the air, and they infect all forms of life. Their sequences are even found in most eukaryotic genomes
What are endogenous retroviruses?
Endogenous retroviruses alter the DNA of the organism they infect, and then this trait is passed down. Endogenous retroviruses actually make up 5-8% of the human genome sequence
You should understand the basic concept of epidemic diseases and their impacts on us
- 1918 flu epidemic - dropped life expectancy
- smallpox - led to the development of the first vaccines
- Polio - killed and paralyzed hundreds of thousands, caused mass panic
- HIV - has helped to impoverish Africa
How have viruses impacted our knowledge of our own cells?
they have helped us learn a lot about our own cells (transcription factors, mRNA processing, etc.)
What are the four ways that viruses can be useful to us?
- can help us identify certain species of bacteria via phage typing
- used as a pesticide and anti-bacterial agent
- development as an anti-cancer agent
- gene therapy - using genetically engineered viruses as gene delivery agents
Know the three major hypothesis that explain where viruses came from and know some of the pieces of evidence that support each theory
- self-replicating RNA
- a piece of a cell may have split off from the rest and that piece is what then became a virus
- a cell that lost most of its function and structure
hypothesis #1 : self-replicating DNA
evidence: early RNA had enzymatic activity and the ability to self-replicate, like modern viroids
- it’s possible that one of these invaded an early cell and gained capsid shells
hypothesis #2 : a piece of a cell may have split off from the rest and that piece is what then became a virus
evidence : many viral genomes strongly resemble mRNA
Transposon
a piece of DNA that can cut itself out and insert itself somewhere else
Viroids
small bits of RNA that have the ability to copy themselves
Plasmids
small, circular DNAs that can self-replicate and sometimes move from cell to cell on their own
hypothesis #3 : a cell that lost most of its function and structure
evidence : mitochondria were once prokaryotic symbionts that lost the ability to live independently, so maybe viruses arose through similar loss of function
Why do scientists think that viruses evolved separately in different hosts?
Genome type and structure are often host-specific (ex. plant viruses have ssRNA, while fungal viruses have dsRNA)
Know the major events in virology history, 1 : cause of tobacco disease
they took extract of a diseased plant and put it through a filter with tiny holes that bacteria could not pass through. They theorized that there was an agent causing the disease to fit through
Know the major events in virology history, 2 : a similar agent was found to be responsible for foot-and-mouth disease
animals could contract viruses
Know the major events in virology history, 3 : viruses can cause disease in humans
yellow fever ; also, viruses could be transmitted by vectors
Know the major parts of virion and be able to draw them and their locations
- genome
- capsid : protein shell that protects the genome
additional parts of some visions: - matrix : layer of proteins b/t capsid and envelope
- envelope : outer membrane
What are viral genomes made of and what do they look like structurally?
- Know all of the varieties
- use either DNA or RNA
- can be single-stranded or double-stranded
- can be linear or circular
What are segmented genomes? What are their advantages and drawbacks?
the genome is split into different pieces of nucleic acid
- advantages : can create new combinations of segments when two viruses co-infect a cell
- disadvantages : have to package multiple genomic pieces into the same capsid, or plan on infecting each cell with multiple copies of virion
How are some viral genomes modified?
they are modified at their ends
- RNA viruses often have a 5’ cap or 3’ poly A tail
- DNA viruses can have capped RNA primer at its end, to facilitate DNA replication
What types of proteins that are bound to viral genomes?
host proteins (histones) and viral proteins (viral polymerases, etc.)
How do single-stranded genomes fold in on themselves? What two types of structures form when single-stranded genomes fold in on themselves? Understand the basics of how each form.
- by forming H bonds b/t complementary sections w/in the same strand, they can form secondary structures called stem loops
– when stem-loops interact with other parts of the strand, they can form pseudoknots
How big are viral genomes (generally) and how do they maximize space?
- the smallest viruses have just a couple of genes, while the largest are bigger than some prokaryotic genomes
- smaller genomes maximize space by using overlapping reading frames (ORFs)
What are consensus and terminal repeat sequences and what are they used for?
consensus sequences code for promoters, binding sites for proteins etc.
– they are needed for basic DNA replication/transcription
repeated sequences (direct vs indirect) are often used as binding sites for proteins involved in DNA replication or transcription
What is the difference between positive and negative sense RNA genomes?
- with positive sense RNA, ribosomes can bind directly to the genome and translate it into protein
- with negative sense RNA, the genome is opposite sense of mRNA, so it needs to make a complementary and sense copy in order for translation to occur
Understand the difference between virion proteins and those viral proteins that are not packaged into virions
- virion proteins that get packaged into virions are also called structural proteins
- viral proteins that are not packaged into virions are also called non-structural proteins
– these are pressed in infected cells, but are never found in virions - both types are critical for an infection
What is a capsid in general and what are its functions?
- protein shell that surround the viral genome
– protects it
– helps move genome w/in newly infected cells
– in naked viruses, find/attach to outside of target cells
How diverse is the protein composition of most capsids and how do they come together (does something else build them or do they self assemble)?
Capsids are composed of many copies of 1-3 types of proteins, and they self-assemble into multimers
What do helical capsids look like and how do they form around the genome?
capsid proteins self-assemble around the shape of the genome and form a structure similar to the shape of a straw
Icosahedral capsids – how many faces, vertices, and axes of symmetry
20 faces, each an equilateral triangle
12 vertices
3 axes of symmetry : 2-, 3-, and 5-fold
- When does the genome get packaged into icosahedral capsids – before or after it is assembled?
icosahedral capsids often form before the genome is assembled
What is relationship between protein, protomer, capsomere, and capsid?
1) individual proteins aggregate into small protomers
2) protomers assemble into capsomeres
3) protomers and capsomeres together form a capsid
What are spike/fiber proteins, where are they located, and what is their function?
spike/fiber proteins are protein protrusions at the vertices of naked virus capsids, and their function is attachment
What is meant by a pleomorphic capsid?
variable-shaped capsids; they don’t all look the same
What is a nucleocapsid?
name for the capsid and genome together
What is the envelope, how is it acquired, and where is it acquired?
- an envelope is a protective lipid bilayer around the nucleocapsid
- nucleocapsids acquire it by pushing through the membrane
Know the protein composition of the envelope (host vs viral proteins)
many viral proteins and a few host proteins
What are lipid rafts and what is their significance to viral budding?
special membranes that are rich in cholesterol and receptors
- viral proteins/genome target these lipid rafts during assembly
What is the matrix/tegument and where is it located?
the matrix is an additional layer of protein between the nucleocapsid and envelope
What are the major functions of matrix proteins?
- helps direct the nucleocapsid to the right membrane during budding
- alter host cell metabolism early after viral entry
- help move nucleocapsid following entry
What are occlusion bodies and what are their functions?
occlusion bodies (OBs) are thick crystals of protein outside of host cells that provide an extra layer of protection
What are some of the other molecules that are packaged into virions and what are their functions?
- nongenomic RNA : can be attached to the viral DNA genome and be used to prime replication during entry
- polyamines that bind to viral DNA and protect it, and help it get packaged into capsids
What are major physical characteristics used to classify viruses?
genome type, capsid symmetry presence of an envelope, and presence/absence of unique enzymes
Understand the basics of the taxonomic system – orders, families, etc.
order -> families (viridae) -> genus -> species
Viral families end in what suffix?
viridae
How does the Baltimore classification scheme organize viruses?
viruses are grouped based on how they produce mRNA
What are some of the other properties used to classify viruses (non-structural)?
- host range of the virus
- type of disease it causes
- mode of transmission
- speed of infection
Why is viral spread so important?
if there were no spread, the virus would go “extinct” as hosts die off
What are the two major types of viral spread?
1) spread within a single multicellular host
2) host-host transmission
Cell free virions
- What occurs during this mode of spread?
virions exit one cell, diffuse to cells nearby or distantly, and attach to new cell receptors
Cell-free virions
- When is this type of spread beneficial? What are some of its drawbacks?
- best mechanism for when viruses need to infect multiple tissues in the same organism
- if a virus is unstable, cell-free transmission is risky because you don’t want the capsid to fall apart
Cell-cell contact
- Why is this needed in some cases?
- What are its benefits?
- some viruses may have unstable virions or don’t release a lot of virions
- benefits:
– can avoid host immune components
– can spread very quickly laterally w/in a tissue
– good for viruses that replicate slowly or have low infectivity
Cell-cell contact
- How was it discovered?
discovered by adding antibodies specific for viral glycoproteins, and noted that some viruses still spread
- What are the four main mechanisms of cell-cell contact? Understand what occurs during each process. (1-2)
1) target intracellular junctions where cells are in very close proximity
– virions spread laterally w/in a tissue
2) use existing adhesion synapses or induce new ones
– Some viruses will trigger increases in surface adhesion proteins in infected cells
– makes them “stickier” to nearby uninfected cells
- What are the four main mechanisms of cell-cell contact? Understand what occurs during each process. (3-4)
3) use host cytoskeletal proteins to propel themselves into adjacent cells
4) induction of syncytia
– infected cells bind and fuse to noninflected cells resulting in one large cell with many nuclei
Genome integration
- What occurs in this type of mode of transmission?
- What types of viruses use this?
- retroviruses and lysogenic bacteriophages integrate their genome into host cell gamete
– when cells replicate, the viral genome will be copied and replicated as well
Genome integration
- Why is it beneficial?
- most effective way of spreading w/o the immune system finding them
